Great news especially for plant labs! Researchers from BGI, and their collaborators, have shown that using the restriction enzyme MspJI upstream of next generation sequencing, is very effective to produce high resolution, ~50% representative plant methylomes. MspJI-seq Arabidopsis methylome data was BETTER than MeDIP-seq and MBD-seq data. MspJI-seq data sensitivity and specificity was comparable with whole genome bisulfite sequencing, (WGBS) data. Geneticists have used Arabidopsis, as a model organism, to produce much of the basic knowledge concerning DNA methylation in plants. However, most plants generally have very large and repetitive genomes – compared to mammalian cells. That translates into very large price tags for bisulfite sequencing. (Yikes!) The BGI authors stated that they have produced a plant methylome mapping method that could “be feasible, reliable, and economical in methylation investigation.”
So what do botanists know about plant DNA methylation? Cytosine methylation in plants occurs at CpG, CHG and CHH sequences. “H” standing for A,C or T. DNA methylation has been shown to have critical roles in plant environmental response and development. Methylomes can affect plants across generations. Methylation also functions to protect plant genomes from transposons which can reek havoc on plant chromosomes.
MspJI-seq is an avenue for further plant methylome research. More work is needed to show how all of these downstream effects are produced exactly. As well as what mechanisms control plant DNA de-methylation. I’d love to see the MspJI-seq method applied to crop plants, i.e. rice, maize. Also, I read that some epigenetic processes are shared with mammals. It can be easier to use plants as models to study the impact of these processes in human diseases.
Please have a look at this paper to learn the method details. Huang X, Lu H, Wang JW, Xu L, Liu S, Sun J, Wang J, Gao F. High-throughput sequencing of methylated cytosine enriched by modifcation-dependent restriction endonuclease Msp JI. (2013) BMC Genet.